In Kaluza-Klein theories of low-scale quantum gravity, gravitons and isosinglet neutrinos may propagate in a higher-dimensional space with large compact dimensions, whereas all particles of the Standard Model are confined on a (1+3)-dimensional subspace. After compactification of the extra dimensions, the resulting Yukawa couplings of the Kaluza-Klein neutrinos to the lepton doublets become naturally very suppressed by a higher-dimensional volume factor, in agreement with phenomenological observations. We show that one-loop effects induced by Kaluza-Klein neutrinos, albeit tiny individually, act cumulatively in electroweak processes, giving rise to a non-decoupling behaviour for large values of the higher-dimensional Yukawa couplings. Owing to the non-decoupling effects of Kaluza-Klein neutrinos, we can derive stronger constraints on the parameters of the theory that originate from the non-observation of flavour-violating and universality-breaking phenomena, which involve the W and Z bosons, and the e, $mu$ and $tau$ leptons.